addGraph: Add graphs to RedeR application.

In RedeR: Interactive visualization and manipulation of nested networks

Description

Method to wrap R graphs into RedeR objects and send it to RedeR app.

Usage

addGraph(obj, g, ...)

Arguments

obj	Object of RedPort Class.
g	An igraph object.
...	Additional arguments passed to RedeR application.

Details

Additional arguments:

layout

Vertex coordinates (graph layout). Accepts matrix with 2 cols (i.e. x and y coords) <matrix>.

gscale

Expansion factor of the graph area related to the app panel area (default = 75) <numeric>.

zoom

Sets the zoom scale for the app panel (range: 0.0 to 100.0; default = 100.0) <numerics>.

gcoord

Sets the graph x,y center. Coords between 0 and 100 are set to the visible area of the app panel (default = c(50,50)) <numeric vector>.

isNest

Logical value, whether to nest all nodes into a new container (default = FALSE). See additional args in nestNodes

isAnchor

If isNest=TRUE, this logical value sets whether to anchor the container in dynamic layouts (default = TRUE).

isAssign

If isNest=TRUE, this logical value sets whether to assign the container name to the nested nodes (default = FALSE).

loadEdges

Logical value, whether to send edges to RedeR app (default = TRUE).

theme

Some pre-defined nest attributes. Options: 'tm0','tm1','tm2','tm3','tm4','tm5','tm6' <string>. Alternatively, it can be a list with customized attributes.

ntransform

Logical value, whether to transform nodes in containers (default = FALSE).

parent

ID of a container already available in the app <string>. Nodes from g will be nested to this container.

Value

Submits R graphs to RedeR app.

Attributes passed by the igraph object

Graph attributes

bgColor

Sets the background color of the app panel <hexadecimal>.

zoom

Sets the zoom scale for the app panel (range: 0.0 to 100.0) (Default=100) <numerics>.

gscale

Expansion factor of the graph area related to the app panel (range: 0.0 to 100.0) (Default=100) <numerics> (PS. alternative entry to the 'gscale' argument above).

coordX

Sets the graph x center; x between 0 and 100 sets to visible area <numeric> (PS. alternative entry to the 'gcoord' argument above).

coordY

Sets the graph y center; y between 0 and 100 sets to visible area <numeric> (PS. alternative entry to the 'gcoord' argument above).

loadEdges

Logical value, whether to send edges to RedeR app (Default=TRUE) (PS. alternative entry to the 'loadEdges' argument above).

isNest

Logical value, whether to nest all nodes into a new container (Default=FALSE) (PS. alternative entry to the 'nest' argument above).

isAnchor

If isNest=TRUE, this logical value sets whether to anchor the container in dynamic layouts (Default=FALSE).

isAssign

If isNest=TRUE, this logical value sets whether to assign the container name to the nested nodes (Default=FALSE).

nestColor

If isNest=TRUE, this attribute sets the 'color' of the new container <hexadecimal>.

nestAlias

If isNest=TRUE, this attribute sets the label of the new container <string>.

nestFontSize

If isNest=TRUE, this attribute sets the size of the container label (Default=12). <numerics>.

nestFontColor

If isNest=TRUE, this attribute sets the 'color' of the container label <hexadecimal>.

nestFontX

If isNest=TRUE, this attribute sets the x position of the label related to the container (Default=-8) <numerics>.

nestFontY

If isNest=TRUE, this attribute sets the y position of the label related to the container (Default=-8) <numerics>.

nestShape

If isNest=TRUE, this attribute sets the shape of the container, options: <'ELLIPSE'> and <'ROUNDED_RECTANGLE'> (Default= ELLIPSE).

nestSize

If isNest=TRUE, this attribute sets the size of the container (Default=NULL) <numerics>.

nestLineWidth

If isNest=TRUE, this attribute sets the line width of the container, options: >= 0 (Default=1.0) <numerics>.

nestLineColor

If isNest=TRUE, this attribute sets the line color of the container <hexadecimal>.

nestImage

If isNest=TRUE, sets the status of the container on the screen: <'plain'>, <'transparent'>, or <'hide'> (Default= plain).

nestLineType

If isNest=TRUE, this attribute sets the line type of the container: <'SOLID'>, <'DOTTED'>, <'DOTTED_SHORT'>, <'LONG_DASH'> (Default='SOLID').

Vertex attributes

name

Node attribute 'name' <string>.

nodeAlias

Node attribute 'alias' <string>.

nodeBend

Node attribute 'bend', options: 0-100% (Default=50) <numeric>.

coordX

Node attribute 'x coord' (Default=random coord) <numeric>.

coordY

Node attribute 'y coord'(Default=random coord) <numeric>.

nodeSize

Node attribute 'size', options: > 0 (Default=20) <numeric>.

nodeShape

Node attribute 'shape', options: 'ELLIPSE', 'RECTANGLE', 'ROUNDED_RECTANGLE', 'TRIANGLE', 'DIAMOND' (Default= ELLIPSE) <string>.

nodeColor

Node attribute 'color', e.g. "#ff0000" for red <hexadecimal>.

nodeWeight

Node attribute 'weight', options: >= 0 (Default=0) <numeric>.

nodeLineWidth

Node attribute 'line width', options: >= 0 (Default=1) <numeric>.

nodeLineColor

Node attribute 'line color', e.g. "#ff0000" for red <hexadecimal>.

nodeFontSize

Node attribute 'font size', options: >= 0 (Default=12) <integer>.

nodeFontColor

Node attribute 'font color', e.g. "#ff0000" for red <hexadecimal>.

Edge attributes

arrowDirection

Edge attribute 'arrow direction', used to set mixed associations in undirected graphs. Options: 0 (A-B), 1 (A-> B), -1 (A-| B), 2 (A <-B), -2 (A |-B), 3 (A <-> B), -3 (A |-| B), 4 (A |-> B) and -4 (A <-| B) (Default=0) <integer>.

arrowType

Edge attribute 'arrow type', used to set the association mode in directed graphs. Options: -1, 0 and 1 (Default=1) <integer>.

edgeWeight

Edge attribute 'weight', options: >= 0 (Default=0.0) <numeric>.

edgeWidth

Edge attribute 'width', options: >=0 (Default=1.0) <numeric>.

edgeColor

Edge attribute 'color', e.g. "#ff0000" for red <hexadecimal>.

edgeType

Edge attribute 'color', options: 'SOLID', 'DOTTED, 'DOTTED_SHORT', 'LONG_DASH' (Default='SOLID').

arrowLength

Edge arrow attribute 'length', options: > 0 (Default=10) <numeric>.

arrowAngle

Edge arrow attribute 'angle', options: 0-90 (Default=45) <numeric>.

linkType

Set assignment type either between nodes and containers or containers and containers. Options: 'nested' and 'notnested' (Default='nested') <string>.

Note

In 'igraph' package, vertex and edge attributes can be assigned as arbitrary R objects. In order to pass these extensible features to RedeR the attributes must be provided in a valid syntax (see above). Only UNIQUE edges are accepted. If present, mutual/multiple edges will be collapsed to unique edges. In this cases, source-target information is transferred to 'arrowDirection' attribute; other attributes will be related to the first edge from the edge list.

Author(s)

Mauro Castro

See Also

getGraph addLegend nesthc nestNodes mergeOutEdges relax selectNodes att

Examples

# Initialize igraph
library(igraph)

## Not run: 

rdp <- RedPort()
calld(rdp)

###

g1 <- graph.empty(n=10, directed=FALSE)
addGraph( rdp, g1, layout.random(g1) )

resetd(rdp)

###

g2 <- graph.lattice(c(5,5,5))
addGraph( rdp, g2, layout.kamada.kawai(g2) )

resetd(rdp)

###

g <- barabasi.game(10)
V(g)$name<-letters[1:10]
V(g)$nodeSize<-c(100,rep(30,9))
addGraph( rdp,  g, ntransform=TRUE )

sg <- barabasi.game(3)
addGraph( rdp, sg, parent="a" )

resetd(rdp)

###...to check loading an interactome!

data(hs.inter)
system.time( addGraph(rdp, hs.inter, layout=NULL) )

## End(Not run)

RedeR documentation built on Nov. 8, 2020, 7:45 p.m.